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Segfaults in utils/test_streamio.py #1534

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utkbansal opened this Issue Jul 20, 2017 · 5 comments

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utkbansal commented Jul 20, 2017

As seen in #1472 there are segfaults if we try to run some tests in test_streamio.py. The current fix is to just mark those tests for skipping.

The travis log for the old numpy build

____________________ MDAnalysisTests/utils/test_streamio.py ____________________
[gw0] linux2 -- Python 2.7.13 /home/travis/miniconda/envs/test/bin/python
Slave 'gw0' crashed while running 'MDAnalysisTests/utils/test_streamio.py::TestNamedStream_filename_behavior::()::test_expanduser_noexpansion_returns_NamedStream'
____________________ MDAnalysisTests/utils/test_streamio.py ____________________
[gw2] linux2 -- Python 2.7.13 /home/travis/miniconda/envs/test/bin/python
Slave 'gw2' crashed while running 'MDAnalysisTests/utils/test_streamio.py::TestNamedStream_filename_behavior::()::test_expandvars'
____________________ MDAnalysisTests/utils/test_streamio.py ____________________
[gw3] linux2 -- Python 2.7.13 /home/travis/miniconda/envs/test/bin/python
Slave 'gw3' crashed while running 'MDAnalysisTests/utils/test_streamio.py::TestNamedStream_filename_behavior::()::test_expandvars_noexpansion_returns_NamedStream'
============== 3 failed, 5123 passed, 1 skipped in 560.61 seconds ==============

There is also a comment in the tests by @orbeckst Segmentation fault when run as a test on Mac OS X 10.6, Py 2.7.11 [orbeckst]

utkbansal added a commit to utkbansal/mdanalysis that referenced this issue Jul 20, 2017

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kain88-de Jul 20, 2017

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i'd be interested to see if these segfaults still occur with python 3.6

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kain88-de commented Jul 20, 2017

i'd be interested to see if these segfaults still occur with python 3.6

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richardjgowers Jul 20, 2017

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I don't think they do, which I suspect is something to do with how namedstream uses os.PathLike, or whatever the changes in 3.6 were related to strings/streams/paths.

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richardjgowers commented Jul 20, 2017

I don't think they do, which I suspect is something to do with how namedstream uses os.PathLike, or whatever the changes in 3.6 were related to strings/streams/paths.

kain88-de added a commit that referenced this issue Jul 20, 2017

Pytest Style: test_streamio.py (#1472)
* Pytest Style test_streamio.py

* Fix yield based tests

* Use tmpdir

* Adds skipif

* Refer issue #1534 for segfaults

@orbeckst orbeckst added the testing label Jul 21, 2017

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orbeckst Aug 21, 2017

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Is this still a problem?

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orbeckst commented Aug 21, 2017

Is this still a problem?

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orbeckst Sep 12, 2017

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@richardjgowers @kain88-de should we close this?

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orbeckst commented Sep 12, 2017

@richardjgowers @kain88-de should we close this?

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orbeckst Nov 22, 2017

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Just to answer my question: the tests are currently skipped. It needs to be evaluated if they still produce segfaults and if so, what the deeper reason is.

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orbeckst commented Nov 22, 2017

Just to answer my question: the tests are currently skipped. It needs to be evaluated if they still produce segfaults and if so, what the deeper reason is.

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